MMOD: an R library for the calculation of population differentiation statistics

被引：258
作者：
Winter, David J. [1 ]
机构：
[1] Univ Otago, Dept Zool, Allan Wilson Ctr Mol Ecol & Evolut, Dunedin 9016, New Zealand
来源：
MOLECULAR ECOLOGY RESOURCES | 2012年 / 12卷 / 06期
关键词：
D est; G?ST; G ST; f'ST; empirical population genetics; R; differentiation; GENOTYPE; GENETICS; PACKAGE; G(ST);
D O I：
10.1111/j.1755-0998.2012.03174.x
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
mmod is a library for the R programming language that allows the calculation of the population differentiation measures Dest, G?ST and f'ST. R provides a powerful environment in which to conduct and record population genetic analyses but, at present, no R libraries provide functions for the calculation of these statistics from standard population genetic files. In addition to the calculation of differentiation measures, mmod can produce parametric bootstrap and jackknife samples of data sets for further analysis. By integrating with and complimenting the existing libraries adegenet and pegas, mmod extends the power of R as a population genetic platform.
引用
收藏
页码：1158 / 1160
页数：3
相关论文
共 26 条
[11]  
Hedrick PW, 1999, EVOLUTION, V53, P313, DOI [10.1111/j.1558-5646.1999.tb03767.x, 10.2307/2640768]
[12]   A standardized genetic differentiation measure [J].
Hedrick, PW .
EVOLUTION, 2005, 59 (08) :1633-1638
[13]   adegenet:: a R package for the multivariate analysis of genetic markers [J].
Jombart, Thibaut .
BIOINFORMATICS, 2008, 24 (11) :1403-1405
[14]   GST and its relatives do not measure differentiation [J].
Jost, Lou .
MOLECULAR ECOLOGY, 2008, 17 (18) :4015-4026
[15]   Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species [J].
Kosman, E ;
Leonard, KJ .
MOLECULAR ECOLOGY, 2005, 14 (02) :415-424
[16]   Using the AMOVA framework to estimate a standardized genetic differentiation measure [J].
Meirmans, Patrick G. .
EVOLUTION, 2006, 60 (11) :2399-2402
[17]   Assessing population structure: FST and related measures [J].
Meirmans, Patrick G. ;
Hedrick, Philip W. .
MOLECULAR ECOLOGY RESOURCES, 2011, 11 (01) :5-18
[18]   GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms [J].
Meirmans, PG ;
Van Tienderen, PH .
MOLECULAR ECOLOGY NOTES, 2004, 4 (04) :792-794
[19]   ANALYSIS OF GENE DIVERSITY IN SUBDIVIDED POPULATIONS [J].
NEI, M .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1973, 70 (12) :3321-3323
[20]   ESTIMATION OF FIXATION INDEXES AND GENE DIVERSITIES [J].
NEI, M ;
CHESSER, RK .
ANNALS OF HUMAN GENETICS, 1983, 47 (JUL) :253-259
123